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Rara retinoic acid receptor, alpha [ Mus musculus (house mouse) ]

Gene ID: 19401, updated on 8-May-2016
Official Symbol
Raraprovided by MGI
Official Full Name
retinoic acid receptor, alphaprovided by MGI
Primary source
MGI:MGI:97856
See related
Ensembl:ENSMUSG00000037992 Vega:OTTMUSG00000006440
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
RAR; Nr1b1; RARalpha1
Orthologs
Location:
11 62.76 cM; 11 D-E1
Exon count:
18
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 11 NC_000077.6 (98927809..98974942)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (98799010..98836256)

Chromosome 11 - NC_000077.6Genomic Context describing neighboring genes Neighboring gene WAS/WASL interacting protein family, member 2 Neighboring gene cell division cycle 6 Neighboring gene predicted gene, 38986 Neighboring gene gap junction protein, delta 3 Neighboring gene topoisomerase (DNA) II alpha

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
alpha-actinin binding ISO
Inferred from Sequence Orthology
more info
 
chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
 
drug binding ISO
Inferred from Sequence Orthology
more info
 
enzyme binding ISO
Inferred from Sequence Orthology
more info
 
histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
mRNA 5'-UTR binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol 3-kinase regulator activity ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
protein kinase A binding ISO
Inferred from Sequence Orthology
more info
 
protein kinase B binding ISO
Inferred from Sequence Orthology
more info
 
receptor binding ISO
Inferred from Sequence Orthology
more info
 
regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid binding ISO
Inferred from Sequence Orthology
more info
 
retinoic acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid receptor activity ISO
Inferred from Sequence Orthology
more info
 
retinoic acid-responsive element binding ISO
Inferred from Sequence Orthology
more info
 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription coactivator activity ISO
Inferred from Sequence Orthology
more info
 
transcription corepressor activity ISO
Inferred from Sequence Orthology
more info
 
transcription factor activity, sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
translation repressor activity, nucleic acid binding ISO
Inferred from Sequence Orthology
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Sertoli cell fate commitment IMP
Inferred from Mutant Phenotype
more info
PubMed 
apoptotic cell clearance ISO
Inferred from Sequence Orthology
more info
 
bone development IGI
Inferred from Genetic Interaction
more info
PubMed 
cellular response to estrogen stimulus ISO
Inferred from Sequence Orthology
more info
 
cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
chondroblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic camera-type eye development IGI
Inferred from Genetic Interaction
more info
PubMed 
face development IGI
Inferred from Genetic Interaction
more info
PubMed 
germ cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
glandular epithelial cell development IGI
Inferred from Genetic Interaction
more info
PubMed 
growth plate cartilage development IGI
Inferred from Genetic Interaction
more info
PubMed 
limb development IGI
Inferred from Genetic Interaction
more info
PubMed 
male gonad development ISO
Inferred from Sequence Orthology
more info
 
multicellular organism growth IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of apoptotic process IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of granulocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of interferon-gamma production ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
negative regulation of translation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of translational initiation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor production ISO
Inferred from Sequence Orthology
more info
 
neural tube closure IGI
Inferred from Genetic Interaction
more info
PubMed 
outflow tract septum morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade ISO
Inferred from Sequence Orthology
more info
 
positive regulation of T-helper 2 cell differentiation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of binding ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell cycle ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-13 production ISO
Inferred from Sequence Orthology
more info
 
positive regulation of interleukin-4 production ISO
Inferred from Sequence Orthology
more info
 
positive regulation of interleukin-5 production ISO
Inferred from Sequence Orthology
more info
 
positive regulation of neuron differentiation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of phosphatidylinositol 3-kinase signaling ISO
Inferred from Sequence Orthology
more info
 
positive regulation of protein kinase B signaling ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
regulation of granulocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of myelination ISO
Inferred from Sequence Orthology
more info
 
regulation of phosphatidylinositol 3-kinase activity ISO
Inferred from Sequence Orthology
more info
 
regulation of synaptic plasticity ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
response to ethanol ISO
Inferred from Sequence Orthology
more info
 
response to retinoic acid IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to retinoic acid ISO
Inferred from Sequence Orthology
more info
 
retinoic acid receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
signal transduction ISO
Inferred from Sequence Orthology
more info
 
spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
trachea cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
ureteric bud development IMP
Inferred from Mutant Phenotype
more info
PubMed 
ventricular cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
actin cytoskeleton ISO
Inferred from Sequence Orthology
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
dendrite IDA
Inferred from Direct Assay
more info
PubMed 
dendrite ISO
Inferred from Sequence Orthology
more info
 
neuron projection ISO
Inferred from Sequence Orthology
more info
 
neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 
Preferred Names
retinoic acid receptor alpha
Names
RAR alpha 1
RAR-alpha
nuclear receptor subfamily 1 group B member 1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001176528.1NP_001169999.1  retinoic acid receptor alpha isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 5' sequence including the 5' CDS, as compared to variant 1. The resulting isoform (2) has a shorter and different N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL591067
    Consensus CDS
    CCDS48905.1
    UniProtKB/Swiss-Prot
    P11416
    Related
    ENSMUSP00000103097, OTTMUSP00000006837, ENSMUST00000107473, OTTMUST00000014709
    Conserved Domains (2) summary
    cd06937
    Location:183413
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:79163
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. NM_001177302.1NP_001170773.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_001170773.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an additional exon in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform 1.
    Source sequence(s)
    AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000069744, OTTMUSP00000006834, ENSMUST00000068133, OTTMUST00000014706
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  3. NM_001177303.1NP_001170774.1  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_001170774.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon, as compared to variant 1. Variants 1-3 encode the same isoform 1.
    Source sequence(s)
    AK042163, AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000129791, ENSMUST00000164748
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  4. NM_009024.2NP_033050.2  retinoic acid receptor alpha isoform 1

    See identical proteins and their annotated locations for NP_033050.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK042163, AL591067
    Consensus CDS
    CCDS36304.1
    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000103099, OTTMUSP00000006835, ENSMUST00000107475, OTTMUST00000014707
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000077.6 Reference GRCm38.p3 C57BL/6J

    Range
    98927809..98974942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006532592.2XP_006532655.1  

    See identical proteins and their annotated locations for XP_006532655.1

    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Related
    ENSMUSP00000103098, OTTMUSP00000006836, ENSMUST00000107474, OTTMUST00000014708
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  2. XM_011248825.1XP_011247127.1  

    See identical proteins and their annotated locations for XP_011247127.1

    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  3. XM_006532591.2XP_006532654.1  

    See identical proteins and their annotated locations for XP_006532654.1

    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  4. XM_006532594.2XP_006532657.1  

    See identical proteins and their annotated locations for XP_006532657.1

    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  5. XM_006532593.2XP_006532656.1  

    See identical proteins and their annotated locations for XP_006532656.1

    UniProtKB/Swiss-Prot
    P11416
    UniProtKB/TrEMBL
    Q3U3R3
    Conserved Domains (3) summary
    cd06937
    Location:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    pfam11936
    Location:1968
    DUF3454; Domain of unknown function (DUF3454)
  6. XM_006532598.2XP_006532661.1  

    See identical proteins and their annotated locations for XP_006532661.1

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  7. XM_006532597.2XP_006532660.1  

    See identical proteins and their annotated locations for XP_006532660.1

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  8. XM_006532596.2XP_006532659.1  

    See identical proteins and their annotated locations for XP_006532659.1

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  9. XM_006532595.2XP_006532658.1  

    See identical proteins and their annotated locations for XP_006532658.1

    UniProtKB/TrEMBL
    Q3U5E7
    Conserved Domains (2) summary
    cd06937
    Location:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:144
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

Alternate Mm_Celera

Genomic

  1. AC_000033.1 Alternate Mm_Celera

    Range
    108602792..108640796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)